Directed evolution effectively selects for DNA based physical reservoir computing networks capable of multiple tasks
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| Format: | Preprint |
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2025
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| _version_ | 1866915625204449280 |
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| author | Pandey, Tanmay Feketa, Petro Steinkühler, Jan |
| author_facet | Pandey, Tanmay Feketa, Petro Steinkühler, Jan |
| contents | DNA and other biopolymers are being investigated as new computing substrates and alternative to silicon-based digital computers. However, the established top-down design of biomolecular interaction networks remains challenging and does not fully exploit biomolecular self-assembly capabilities. Outside the field of computation, directed evolution has been used as a tool for goal directed optimization of DNA sequences. Here, we propose integrating directed evolution with DNA-based reservoir computing to enable in-material optimization and adaptation. Simulations of colloidal bead networks connected via DNA strands demonstrate a physical reservoir capable of non-linear time-series prediction tasks, including Volterra series and Mackey-Glass chaotic dynamics. Reservoir computing performance, quantified by normalized mean squared error (NMSE), strongly depends on network topology, suggesting task-specific optimal network configurations. Implementing genetic algorithms to evolve DNA-encoded network connectivity effectively identified well-performing reservoir networks. Directed evolution improved reservoir performance across multiple tasks, outperforming random network selection. Remarkably, sequential training on distinct tasks resulted in reservoir populations maintaining performance on prior tasks. Our findings indicate that DNA-bead networks offer sufficient complexity for reservoir computing, and that directed evolution robustly optimizes performance. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2509_04000 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Directed evolution effectively selects for DNA based physical reservoir computing networks capable of multiple tasks Pandey, Tanmay Feketa, Petro Steinkühler, Jan Soft Condensed Matter Disordered Systems and Neural Networks DNA and other biopolymers are being investigated as new computing substrates and alternative to silicon-based digital computers. However, the established top-down design of biomolecular interaction networks remains challenging and does not fully exploit biomolecular self-assembly capabilities. Outside the field of computation, directed evolution has been used as a tool for goal directed optimization of DNA sequences. Here, we propose integrating directed evolution with DNA-based reservoir computing to enable in-material optimization and adaptation. Simulations of colloidal bead networks connected via DNA strands demonstrate a physical reservoir capable of non-linear time-series prediction tasks, including Volterra series and Mackey-Glass chaotic dynamics. Reservoir computing performance, quantified by normalized mean squared error (NMSE), strongly depends on network topology, suggesting task-specific optimal network configurations. Implementing genetic algorithms to evolve DNA-encoded network connectivity effectively identified well-performing reservoir networks. Directed evolution improved reservoir performance across multiple tasks, outperforming random network selection. Remarkably, sequential training on distinct tasks resulted in reservoir populations maintaining performance on prior tasks. Our findings indicate that DNA-bead networks offer sufficient complexity for reservoir computing, and that directed evolution robustly optimizes performance. |
| title | Directed evolution effectively selects for DNA based physical reservoir computing networks capable of multiple tasks |
| topic | Soft Condensed Matter Disordered Systems and Neural Networks |
| url | https://arxiv.org/abs/2509.04000 |